Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable

A Corrigendum to this article was published on 01 February 2012


The small intestine epithelium renews every 2 to 5 days, making it one of the most regenerative mammalian tissues. Genetic inducible fate mapping studies have identified two principal epithelial stem cell pools in this tissue. One pool consists of columnar Lgr5-expressing cells that cycle rapidly and are present predominantly at the crypt base1. The other pool consists of Bmi1-expressing cells that largely reside above the crypt base2. However, the relative functions of these two pools and their interrelationship are not understood. Here we specifically ablated Lgr5-expressing cells in mice using a human diphtheria toxin receptor (DTR) gene knocked into the Lgr5 locus. We found that complete loss of the Lgr5-expressing cells did not perturb homeostasis of the epithelium, indicating that other cell types can compensate for the elimination of this population. After ablation of Lgr5-expressing cells, progeny production by Bmi1-expressing cells increased, indicating that Bmi1-expressing stem cells compensate for the loss of Lgr5-expressing cells. Indeed, lineage tracing showed that Bmi1-expressing cells gave rise to Lgr5-expressing cells, pointing to a hierarchy of stem cells in the intestinal epithelium. Our results demonstrate that Lgr5-expressing cells are dispensable for normal intestinal homeostasis, and that in the absence of these cells, Bmi1-expressing cells can serve as an alternative stem cell pool. These data provide the first experimental evidence for the interrelationship between these populations. The Bmi1-expressing stem cells may represent both a reserve stem cell pool in case of injury to the small intestine epithelium and a source for replenishment of the Lgr5-expressing cells under non-pathological conditions.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Characterization of DT-mediated CBC ablation.
Figure 2: Maintenance of normal crypt architecture is not mediated by Lgr5 -positive cells that have escaped ablation.
Figure 3: Bmi1 -expressing stem cells are mobilized to compensate for the loss of Lgr5 -expressing CBCs.
Figure 4: Bmi1- expressing cells give rise to Lgr5- expressing CBCs under normal and injury conditions.


  1. Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5 . Nature 449, 1003–1007 (2007)

    Article  ADS  CAS  Google Scholar 

  2. Sangiorgi, E. & Capecchi, M. R. Bmi1 is expressed in vivo in intestinal stem cells. Nature Genet. 40, 915–920 (2008)

    Article  CAS  Google Scholar 

  3. Li, L. & Clevers, H. Coexistence of quiescent and active adult stem cells in mammals. Science 327, 542–545 (2010)

    Article  ADS  CAS  Google Scholar 

  4. Fuchs, E. The tortoise and the hair: slow-cycling cells in the stem cell race. Cell 137, 811–819 (2009)

    Article  CAS  Google Scholar 

  5. Zhu, L. et al. Prominin 1 marks intestinal stem cells that are susceptible to neoplastic transformation. Nature 457, 603–607 (2009)

    Article  ADS  CAS  Google Scholar 

  6. Furuyama, K. et al. Continuous cell supply from a Sox9-expressing progenitor zone in adult liver, exocrine pancreas and intestine. Nature Genet. 43, 34–41 (2011)

    Article  CAS  Google Scholar 

  7. Sato, T. et al. Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts. Nature 469, 415–418 (2011)

    Article  ADS  CAS  Google Scholar 

  8. Cheng, H. & Leblond, C. P. Origin, differentiation and renewal of the four main epithelial cell types in the mouse small intestine. V. Unitarian Theory of the origin of the four epithelial cell types. Am. J. Anat. 141, 537–561 (1974)

    Article  CAS  Google Scholar 

  9. Montgomery, R. K. et al. Mouse telomerase reverse transcriptase (mTert) expression marks slowly cycling intestinal stem cells. Proc. Natl Acad. Sci. USA 108, 179–184 (2011)

    Article  ADS  CAS  Google Scholar 

  10. Muncan, V. et al. Rapid loss of intestinal crypts upon conditional deletion of the Wnt/Tcf-4 target gene c-Myc . Mol. Cell. Biol. 26, 8418–8426 (2006)

    Article  CAS  Google Scholar 

  11. van der Flier, L. G. et al. Transcription factor achaete scute-like 2 controls intestinal stem cell fate. Cell 136, 903–912 (2009)

    Article  CAS  Google Scholar 

  12. Garcia, M. I. et al. LGR5 deficiency deregulates Wnt signaling and leads to precocious Paneth cell differentiation in the fetal intestine. Dev. Biol. 331, 58–67 (2009)

    Article  CAS  Google Scholar 

  13. Crosnier, C., Stamataki, D. & Lewis, J. Organizing cell renewal in the intestine: stem cells, signals and combinatorial control. Nature Rev. Genet. 7, 349–359 (2006)

    Article  CAS  Google Scholar 

  14. Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009)

    Article  ADS  CAS  Google Scholar 

  15. Park, I. K., Morrison, S. J. & Clarke, M. F. Bmi1, stem cells, and senescence regulation. J. Clin. Invest. 113, 175–179 (2004)

    Article  CAS  Google Scholar 

  16. Hosen, N. et al. Bmi-1-green fluorescent protein-knock-in mice reveal the dynamic regulation of bmi-1 expression in normal and leukemic hematopoietic cells. Stem Cells 25, 1635–1644 (2007)

    Article  CAS  Google Scholar 

  17. van der Flier, L. G., Haegebarth, A., Stange, D. E., van de Wetering, M. & Clevers, H. OLFM4 is a robust marker for stem cells in human intestine and marks a subset of colorectal cancer cells. Gastroenterology 137, 15–17 (2009)

    Article  Google Scholar 

  18. Lobachevsky, P. N. & Radford, I. R. Intestinal crypt properties fit a model that incorporates replicative ageing and deep and proximate stem cells. Cell Prolif. 39, 379–402 (2006)

    Article  CAS  Google Scholar 

  19. Buske, P. et al. A comprehensive model of the spatio-temporal stem cell and tissue organisation in the intestinal crypt. PLOS Comput. Biol. 7, e1001045 (2011)

    Article  CAS  Google Scholar 

  20. Wilson, A. et al. Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair. Cell 135, 1118–1129 (2008)

    Article  CAS  Google Scholar 

  21. Ito, M. et al. Stem cells in the hair follicle bulge contribute to wound repair but not to homeostasis of the epidermis. Nature Med. 11, 1351–1354 (2005)

    Article  CAS  Google Scholar 

  22. Hsu, Y. C., Pasolli, H. A. & Fuchs, E. Dynamics between stem cells, niche, and progeny in the hair follicle. Cell 144, 92–105 (2011)

    Article  CAS  Google Scholar 

  23. Bastide, P. et al. Sox9 regulates cell proliferation and is required for Paneth cell differentiation in the intestinal epithelium. J. Cell Biol. 178, 635–648 (2007)

    Article  CAS  Google Scholar 

  24. Garabedian, E. M., Roberts, L. J., McNevin, M. S. & Gordon, J. I. Examining the role of Paneth cells in the small intestine by lineage ablation in transgenic mice. J. Biol. Chem. 272, 23729–23740 (1997)

    Article  CAS  Google Scholar 

  25. Warming, S., Rachel, R. A., Jenkins, N. A. & Copeland, N. G. Zfp423 is required for normal cerebellar development. Mol. Cell. Biol. 26, 6913–6922 (2006)

    Article  CAS  Google Scholar 

  26. Liu, P., Jenkins, N. A. & Copeland, N. G. A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res. 13, 476–484 (2003)

    Article  CAS  Google Scholar 

  27. Kissenpfennig, A. et al. Dynamics and function of Langerhans cells in vivo: dermal dendritic cells colonize lymph node areas distinct from slower migrating Langerhans cells. Immunity 22, 643–654 (2005)

    Article  CAS  Google Scholar 

  28. Warming, S., Costantino, N., Court, D. L., Jenkins, N. A. & Copeland, N. G. Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res. 33, e36 (2005)

    Article  Google Scholar 

  29. Lee, E. C. et al. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73, 56–65 (2001)

    Article  CAS  Google Scholar 

  30. Van Keuren, M. L., Gavrilina, G. B., Filipiak, W. E., Zeidler, M. G. & Saunders, T. L. Generating transgenic mice from bacterial artificial chromosomes: transgenesis efficiency, integration and expression outcomes. Transgenic Res. 18, 769–785 (2009)

    Article  Google Scholar 

  31. Gregorieff, A. & Clevers, H. In situ hybridization to identify gut stem cells. Curr. Protoc. Stem Cell Biol. Ch. 2, Unit 2F.1. (2010)

  32. Potten, C. S., Gandara, R., Mahida, Y. R., Loeffler, M. & Wright, N. A. The stem cells of small intestinal crypts: where are they? Cell Prolif. 42, 731–750 (2009)

    Article  CAS  Google Scholar 

  33. Bjerknes, M. & Cheng, H. The stem-cell zone of the small intestinal epithelium. I. Evidence from Paneth cells in the adult mouse. Am. J. Anat. 160, 51–63 (1981)

    Article  CAS  Google Scholar 

Download references


We gratefully acknowledge efforts by all the members of the Genentech mouse facility, in particular R. Ybarra and G. Morrow. We are grateful to N. Strauli, D.-K. Tran and A. Rathnayake for assistance with mouse breeding. We thank M. Roose-Girma, X. Rairdan and the members of the embryonic stem cell and microinjection groups for embryonic stem cell work and transgenic line generation and members of the F.J.d.S. laboratory for discussions and ideas. This work was funded in part by the National Institutes of Health through the NIH Director’s New Innovator Award Program, 1-DP2-OD007191 and by R01-DE021420, both to O.D.K.

Author information

Authors and Affiliations



H.T., B.B., S.W., K.G.L. and L.R. designed, performed experiments and collected data. H.T., B.B., O.D.K. and F.J.d.S. designed experiments, analysed the data and wrote the manuscript. O.D.K. and F.J.d.S. are joint senior authors. All authors discussed results and edited the manuscript.

Corresponding authors

Correspondence to Ophir D. Klein or Frederic J. de Sauvage.

Ethics declarations

Competing interests

H.T., S.W., K.G.L., L.R. and F.J.d.S. are employees of Genentech Inc., a member of the Roche Group, and may have an equity interest in Roche.

Supplementary information

Supplementary Figures

The file contains Supplementary Figures 1-8 with legends. (PDF 388 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tian, H., Biehs, B., Warming, S. et al. A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable. Nature 478, 255–259 (2011).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing